tbuckley/cabot-search huggingface dataset:
Abstract 588: Regional administration of IL-12 endowed CAR T cells effectively targets systemic disease
Authors: Hee Jun Lee, Saul Priceman
Journal: Cancer Research (2022)

Abstract While chimeric antigen receptor (CAR) T cell therapy has shown impressive clinical efficacy for hematological malignancies, efficacy remains limited for solid tumors due in large part to the immunosuppressive tumor microenvironment. Tumor-associated glycoprotein 72 (TAG72) is an aberrantly glycosylated protein overexpressed on ovarian cancer and is an exciting target for CAR T cell immunotherapy. Our lab previously developed a second-generation TAG72 CAR T cell product and showed its potency against TAG72-expressing ovarian tumor cells both in vitro and in preclinical mouse models. We report here further modification of our TAG72 CAR T cells, with incorporation of interleukin-12 (IL-12) and interleukin-15 (IL-15), and evaluate the therapeutic benefits in peritoneal ovarian tumor models. In this preclinical study, we build upon our earlier work with in vitro and in vivo evaluation of 9 different second-generation TAG72 CAR constructs varying in single-chain variable fragment, extracellular spacer, transmembrane, and intracellular co-stimulatory domains. We then engineer CAR T cells with two types of cytokines - IL-12 and IL-15 - and put these engineered cells against challenging in vivo tumor models. Through in vitro and in vivo studies, we identified the most optimal construct with which we aim to evaluate in a phase 1 clinical trial targeting TAG72-positive ovarian cancer in early 2022. Despite thorough optimizations to the CAR backbone, CAR T cells can be additionally engineered for improved anti-tumor response. Therefore, we further engineered CAR T cells with IL-12 or IL-15 production that greatly improved the effectiveness of TAG72-CAR T cells in difficult-to-treat in vivo tumor models. We observed that modification of CAR T cells with IL-15 displayed toxicity when regionally delivered in vivo, yet introduction of IL-12 not only demonstrated safe and superior therapeutic responses, but also allowed the regional administration of CAR T cells to address systemic disease. We are now expanding these findings by evaluating these therapies using syngeneic immunocompetent mouse tumor models. The tumor microenvironment (TME) harbors various factors that thwart the killing of tumor cells by CAR T cells. Thus, CAR T cells will likely require further engineering to overcome this barrier. We show that amplifying cytokine pathways is one way to overcome the TME and improve the efficacy of CAR T cell therapy for solid tumors. Citation Format: Hee Jun Lee, Saul Priceman. Regional administration of IL-12 endowed CAR T cells effectively targets systemic disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 588.
Intratumoral Resolution of Driver Gene Mutation Heterogeneity in Renal Cancer Using Deep Learning
Authors: Paul H. Acosta, Vandana Panwar, Vipul Jarmale, Alana Christie, Jay Jasti, Vitaly Margulis, Dinesh Rakheja, John Cheville, Bradley C. Leibovich, Alexander Parker, James Brugarolas, Payal Kapur, Satwik Rajaram
Journal: Cancer Research (2022)

Abstract Intratumoral heterogeneity arising from tumor evolution poses significant challenges biologically and clinically. Dissecting this complexity may benefit from deep learning (DL) algorithms, which can infer molecular features from ubiquitous hematoxylin and eosin (H&amp;E)–stained tissue sections. Although DL algorithms have been developed to predict some driver mutations from H&amp;E images, the ability of these DL algorithms to resolve intratumoral mutation heterogeneity at subclonal spatial resolution is unexplored. Here, we apply DL to a paradigm of intratumoral heterogeneity, clear cell renal cell carcinoma (ccRCC), the most common type of kidney cancer. Matched IHC and H&amp;E images were leveraged to develop DL models for predicting intratumoral genetic heterogeneity of the three most frequently mutated ccRCC genes, BAP1, PBRM1, and SETD2. DL models were generated on a large cohort (N = 1,282) and tested on several independent cohorts, including a TCGA cohort (N = 363 patients) and two tissue microarray (TMA) cohorts (N = 118 and 365 patients). These models were also expanded to a patient-derived xenograft (PDX) TMA, affording analysis of homotopic and heterotopic interactions of tumor and stroma. The status of all three genes could be inferred by DL, with BAP1 showing the highest sensitivity and performance within and across tissue samples (AUC = 0.87–0.89 on holdout). BAP1 results were validated on independent human (AUC = 0.77–0.84) and PDX (AUC = 0.80) cohorts. Finally, BAP1 predictions correlated with clinical outputs such as disease-specific survival. Overall, these data show that DL models can resolve intratumoral heterogeneity in cancer with potential diagnostic, prognostic, and biological implications. Significance: This work demonstrates the potential for deep learning analysis of histopathologic images to serve as a fast, low-cost method to assess genetic intratumoral heterogeneity. See related commentary by Song et al., p. 2672
Abstract 5697: Targeting PARP inhibitor resistance with Polθ inhibitors
Authors: Diana Zatreanu, Helen Robinson, Omar Alkhatib, Marie Boursier, Harry Finch, Lerin Geo, Diego Grande, Vera Grinkevich, Robert Heald, Sophie Langdon, Jayesh Majithiya, Claire McWhirter, Niall Martin, Shaun Moore, Joana Neves, Eeson Rajendra, Marco Ranzani, Theresia Schaedler, Martin Stockley, Kimberley Wiggins, Rachel Brough, Sandhya Sridhar, Aditi Gulati, Nan Shao, Luted Badder, Daniela Novo, Eleanor Knight, Rebecca Marlow, Syed Haider, Elsa Callen, Graeme Hewitt, Joost Schimmel, Remko Prevo, Christina Alli, Amanda Ferdinand, Cameron Bell, Peter Blencowe, Chris Bot, Mathew Calder, Mark Charles, Jayne Curry, Tennyson Ekwuru, Andre Nussenzweig, Marcel Tijsterman, Andrew N. Tutt, Simon Boulton, Geoff Higgins, Stephen J. Pettitt, Graeme C. Smith, Christopher J. Lord
Journal: Cancer Research (2022)

Abstract To target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining (TMEJ), without targeting Non-Homologous End Joining. Moreover, we show that exposure to ART558 can elicit DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumor cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which are a cause of PARP inhibitor resistance, result in in vitro and in vivo sensitivity to Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells. The inhibition of DNA nucleases that promote end-resection, such as Exo1 or Blm-Dna2 reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance. Citation Format: Diana Zatreanu, Helen Robinson, Omar Alkhatib, Marie Boursier, Harry Finch, Lerin Geo, Diego Grande, Vera Grinkevich, Robert Heald, Sophie Langdon, Jayesh Majithiya, Claire McWhirter, Niall Martin, Shaun Moore, Joana Neves, Eeson Rajendra, Marco Ranzani, Theresia Schaedler, Martin Stockley, Kimberley Wiggins, Rachel Brough, Sandhya Sridhar, Aditi Gulati, Nan Shao, Luted Badder, Daniela Novo, Eleanor Knight, Rebecca Marlow, Syed Haider, Elsa Callen, Graeme Hewitt, Joost Schimmel, Remko Prevo, Christina Alli, Amanda Ferdinand, Cameron Bell, Peter Blencowe, Chris Bot, Mathew Calder, Mark Charles, Jayne Curry, Tennyson Ekwuru, Andre Nussenzweig, Marcel Tijsterman, Andrew N. Tutt, Simon Boulton, Geoff Higgins, Stephen J. Pettitt, Graeme C. Smith, Christopher J. Lord. Targeting PARP inhibitor resistance with Polθ inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5697.
Abstract 1805: RAB10, a new target to tackle SMAD4 deficient cancers
Authors: Christophe Marcireau, Hélène Erasimus, Vanessa Kolnik, Frederic Lacroix, Stephane D’agostino, Olivier Lemaitre, Alexandre Rohaut, Isabelle sanchez, Sukhvinder Sidhu, Gilbert Thill, Laurent Debussche, Michel Didier
Journal: Cancer Research (2022)

Abstract TGFb pathway is an important signaling process that regulates the homeostasis of epithelial, stromal or immune cells. Misregulations of this pathway contribute to different pathologies such as cancer, fibrosis, nash or inflammatory diseases. SMAD4 genetic alterations, either via genomic loss or via mutations, can be found in many cancer types. SMAD4 is mutated or deleted in 10-15% of colorectal cancers and in 20-50% of pancreatic cancer. The poorer prognosis of colorectal cancers and pancreatic cancers patients harboring SMAD4 alterations makes SMAD4 deficiency interesting to harness for therapy. Anticancer opportunity created by loss of SMAD4 function/protein could be addressed by identifying synthetic lethal genes that encode for druggable proteins. CRISPR/CAS9 is a revolutionary discovery to produce gene knockout. CRISPR/CAS9 viability screen is a tool of choice to pinpoint new synthetic lethality interactions. In this work, to extend the genetic vulnerabilities of SMAD4-deficient tumors, we conducted a pooled genome-wide loss of function CRISPR/Cas9 screen in sets of 4 non-isogenic colorectal and pancreatic cancers cancer cell lines harboring wild-type and mutant SMAD4. We identified known and novel genetic alterations that make SMAD4-altered colorectal cancers &amp; pancreatic cancers cells vulnerable. We will present the validation of the Ras-related protein Rab-10 (RAB10) as synthetic lethal gene with SMAD4 alteration. Citation Format: Christophe Marcireau, Hélène Erasimus, Vanessa Kolnik, Frederic Lacroix, Stephane D’agostino, Olivier Lemaitre, Alexandre Rohaut, Isabelle sanchez, Sukhvinder Sidhu, Gilbert Thill, Laurent Debussche, Michel Didier. RAB10, a new target to tackle SMAD4 deficient cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1805.
Abstract 1645: Advancing the development of CD16A-based bispecific antibodies in humanized CD16A mouse models
Authors: Jiahui Chang, Tao Li, Limei Ma, Xiaoxia Sun, Yuelei Shen
Journal: Cancer Research (2022)

Abstract Antibody-dependent cell cytotoxicity (ADCC) is an important mechanism in immunotherapy. CD16A (FcγRIIIA), a low-affinity receptor for the IgG Fc domain, facilitates ADCC and is responsible for triggering the lysis of target cells by natural killer (NK) cells. Human CD16A is closely related to mouse Fcgr4 and is expressed in NK cells and macrophages, but is absent in granulocytes. Alternatively, mouse Fcgr4 is expressed in granulocytes and macrophages and is absent in NK cells. CD16A-based bispecific antibodies targeting NK cells have been studied for cancer therapy. To evaluate the anti-tumor efficacy of CD16A-based bispecific antibody in mouse tumor models, we have successfully generated a novel humanized CD16A knock-in mouse strain (B-hCD16A Mice). Considering the differential expression patterns between human CD16A and mouse Fcgr4, the regulatory region and whole genome sequence of mouse Fcgr4 were replaced by the human CD16A gene. Human CD16A and mouse Fcgr4 protein expression was confirmed in heterozygous B-hCD16A mice by FACS and RT-PCR. Human CD16A protein was detected in NK cells and macrophages of B-hCD16A mice, but not granulocytes. When compared with wild type mice, there were no abnormalities in the populations of immune cells in B-hCD16A mice. CD16A-based bispecific antibody usually binds to CD16A on NK cells, whereas the other arm of the antibody binds to tumor antigen on cancer cells. Initial assessment of the tumorigenicity of MC38 cells were evaluated in B-hCD16A mice, and results indicated that these cancer cells were able to establish tumors in vivo. These data suggest that the B-hCD16A mouse model is an effective tool for future in vivo efficacy evaluation of therapeutic CD16A-based bispecific antibodies prior to clinical development. Citation Format: Jiahui Chang, Tao Li, Limei Ma, Xiaoxia Sun, Yuelei Shen. Advancing the development of CD16A-based bispecific antibodies in humanized CD16A mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1645.
Abstract 1024: The challenge of standardizing the measurement of an imprecise biomarker like HRD
Authors: Yves Konigshofer, Matthew G. Butler, Krystyna Nahlik, Dana Ruminski Lowe, Catherine Huang, Omoshile Clement, Russell K. Garlick
Journal: Cancer Research (2022)

Abstract Here we present data on the characterization and implementation of a set of reference materials for the standardization of homologous recombination deficiency (HRD) assessment. The safety and effectiveness profile of a drug can be improved by using it in patients where that drug is most likely to be effective. While PARP inhibitors are indicated for use in some patients with ovarian, breast, pancreatic, and prostate cancer, patients with other cancers that are deficient in homologous recombination repair (HRR) might also benefit from their use. However, determining whether a cancer is HRD-positive is neither trivial nor precise. While clinical trials have shown that patients with deleterious mutations in BRCA2 and BRCA1 are most likely to benefit from PARP inhibitors, determining that a given BRCA mutation (or set of such mutations) is in fact deleterious is frequently not straightforward. Therefore, assays are now looking for signs of HRD, such as genomic instability consistent with non-homologous end joining (NHEJ) being used for the repair of double-stranded breaks in DNA as opposed to HRR. For example, some assays look at the combination of loss of heterozygosity (LOH) and large-scale state transitions (LST) across chromosomes as well as telomeric allelic imbalance (TAI) when determining whether a cancer is HRD-positive, while other assays use alternative approaches. How those characteristics are measured, integrated, and distilled into a final determination of whether HRD is present or absent varies, which can create uncertainty around treatment options and enrollment into clinical trials. This also makes the path of follow-on companion diagnostics challenging because perfect agreement between imprecise measurements is unlikely. In order to enable more standardized reporting of HRD and to enable the assessment of HRD assays, we created a set of characterized reference materials composed of HRD negative, borderline, and positive tumor/normal matched cell lines that were analyzed using both array-based and next generation sequencing-based assays in order to characterize chromosomal changes across their genomes and obtain HRD scores. Because of differences in the results, assay imprecision should be taken into account in clinical trials that implement cutoffs in order to establish safety data for patients who are biomarker-negative but may be biomarker-positive in a future assay, which is similar to what is done for complementary diagnostics. Citation Format: Yves Konigshofer, Matthew G. Butler, Krystyna Nahlik, Dana Ruminski Lowe, Catherine Huang, Omoshile Clement, Russell K. Garlick. The challenge of standardizing the measurement of an imprecise biomarker like HRD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1024.
Cardiorenal Complications in Young-Onset Type 2 Diabetes Compared Between White Americans and African Americans
Authors: Sanjoy K. Paul, Jonathan E. Shaw, Peter Fenici, Olga Montvida
Journal: Diabetes Care (2022)

OBJECTIVE To explore risks and associated mediation effects of developing chronic kidney disease (CKD) and heart failure (HF) in young- and usual-onset type 2 diabetes (T2D) between White Americans (WAs) and African Americans (AAs). RESEARCH DESIGN AND METHODS From U.S. medical records, 1,491,672 WAs and 31,133 AAs were identified and stratified by T2D age of onset (18–39, 40–49, 50–59, 60–70 years). Risks, mediation effects, and time to CKD and HF were evaluated, adjusting for time-varying confounders. RESULTS In the 18–39, 40–49, 50–59, 60–70 age-groups, the hazard ratios (of developing CKD and HF in AAs versus WAs were 1.21 (95% CI 1.17–1.26) and 2.21 (1.98–2.45), 1.25 (1.22–1.28) and 1.86 (1.75–1.97), 1.21 (1.19–1.24) and 1.54 (1.48–1.60), and 1.10 (1.08–1.12) and 1.11 (1.07–1.15), respectively. In AAs and WAs aged 18–39 years, time in years to CKD (8.7 [95% CI 8.2–9.1] and 9.7 [9.2–10.2]) and HF (10.3 [9.3–11.2] and 12.1 [10.6–13.5]) were, on average, 3.6 and 4.0 and 3.1 and 4.1 years longer compared with those diagnosed at age 60–70 years. Compared with females, AA males aged &amp;lt;60 years had an 11–49% higher CKD risk, while WA males aged &amp;lt;40 years had a 23% higher and those aged ≥50 years a 7–14% lower CKD risk, respectively. The mediation effects of CKD on the HF risk difference between ethnicities across age-groups (range 54–91%) were higher compared with those of HF on CKD risk difference between ethnicities across age-groups (13–39%). CONCLUSIONS Developing cardiorenal complications within an average of 10 years of young-onset T2DM and high mediation effects of CKD on HF call for revisiting guidelines on early diagnosis and proactive treatment strategies for effective management of cardiometabolic risk.
Abstract 1597: Characterization of genomic diversity in high grade serous ovarian and triple negative breast cancer at single cell resolution
Authors: Marc J. Williams, Tyler Funnell, Ciara H. O'Flanagan, Andrew McPherson, Samuel Aparicio, Sohrab P. Shah
Journal: Cancer Research (2022)

Abstract Copy number alterations and structural variants are associated with disease progression, therapeutic response, and metastasis in human cancers, yet the extent and mechanisms driving continued genomic instability remain poorly understood. We generated more than 20,000 single-cell whole genomes from 25 high-grade serous ovarian and triple-negative breast cancers across a range of mutational subtypes. Through the development of new computational methods, we resolved alterations into cancer haplotypes, providing fine-grained resolution of genomic events in single-cells and exposing extensive cell-to-cell genomic variation. We identified 3 key processes that contribute to this diversity. Firstly, we observed that parallel copy number events - whereby different cancer cells harbor chromosomal aberrations with identical total copy number but different combinations of maternal and paternal alleles - were present in &amp;gt; 80% of the tumors. This is consistent with extensive convergent evolution in these tumors. Secondly, we identified considerable cell-to-cell variability in the amplitude of high-level amplifications, often impacting oncogenes. Single-cell transcriptomes and immunohistochemistry from the same samples showed that this genomic diversity led to phenotypic differences between cells. Finally, we observed copy number break-point variability consistent with progressive genomic diversification, which we termed serriform structural variation (SSV). Both SSV’s and variable high-level amplifications were enriched in foldback inversion (FBI) bearing tumors relative to homologous recombination deficient tumors, highlighting that FBI tumors have greater levels of structural instability. Our study sheds new light on the evolution of genomically unstable tumors with implications for cancer evolution, therapeutic targeting, and patient stratification. Citation Format: Marc J. Williams, Tyler Funnell, Ciara H. O'Flanagan, Andrew McPherson, Samuel Aparicio, Sohrab P. Shah. Characterization of genomic diversity in high grade serous ovarian and triple negative breast cancer at single cell resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1597.
Abstract 988: Epigenetic upregulation of neuropilin-1 promotes osteosarcoma progression and metastasis
Authors: Niveditha Nerlakanti, Jeremy Mcguire, Diana Yu, Damon Reed, Conor C. Lynch
Journal: Cancer Research (2022)

Abstract Background: Osteosarcoma (OS) frequently metastasizes to lung and the prognosis for these patients is grim with 5-year overall survival rates as low as 30%. There has been little change in the treatment paradigm for this disease and new targeted therapies are an urgent and unmet clinical need. Previously, we showed that the epigenetic regulators, histone deacetylase 1 and 2 (HDAC1 and 2) are key mediators of OS progression and lung metastasis and that the HDAC1/2 selective inhibitor (romidepsin) significantly prevented OS lung metastasis in vivo. Yet, inhibition of HDACs by romidepsin has noted toxicities in humans and here we define the potential mechanisms through which HDAC1/2 mediate their effects in a bid to identify additional therapeutic targets. Methods: Human OS cell lines were treated with vehicle or romidepsin for 24h before undergoing RNA/protein isolation for microarray/proteomics to identify differentially regulated genes. Standard siRNA, proliferation, migration and molecular analyses were preformed to investigate the role of candidate genes in OS malignant behavior. Results: Microarray/proteomics analyses on romidepsin treated OS cells identified neuropilin-1 (NRP1), a membrane bound co-receptor for vascular endothelial growth factor, to be highly downregulated in response to romidepsin; (&amp;lt;70% compared to vehicle in multiple OS cell lines). NRP1 knockdown (siRNA) led to reduced cell proliferation and interestingly, increased cell migration. Further, a phosphokinase array revealed increased phosphorylation in eNOS, ERK 1/2 and β-catenin in NRP1 knockdown cells that is consistent with a role for NRP1 in regulating OS migration. Based on this data, we hypothesize that NRP1 is a significant regulator of OS proliferation and migration. Our next steps will be to dissect the role of NRP1 silencing in OS invasion and metastasisin vivo and the potential role of NRP1 in OS differentiation. Conclusions: HDAC1/2 contributes to OS growth potentially via the upregulation of NRP1, a therapeutically actionable target. Citation Format: Niveditha Nerlakanti, Jeremy Mcguire, Diana Yu, Damon Reed, Conor C. Lynch. Epigenetic upregulation of neuropilin-1 promotes osteosarcoma progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 988.